diff --git a/configure.ac b/configure.ac
index 31e95c05..a2f624f9 100644
--- a/configure.ac
+++ b/configure.ac
@@ -74,8 +74,14 @@ AC_ARG_ENABLE(asm,
 ])
 
 AS_IF([test "x$EMSCRIPTEN" != "x"], [
-  enable_asm="no"
-  AC_MSG_WARN([compiling to JavaScript - asm implementations disabled])
+  AX_CHECK_COMPILE_FLAG([-s ASSERTIONS=0], [
+    enable_asm="no"
+    AC_MSG_WARN([compiling to JavaScript - asm implementations disabled])
+  ], [
+    AC_MSG_WARN([EMSCRIPTEN environment variable defined, but emcc doesn't appear to be used - Assuming compilation to native code])
+    CFLAGS="$CFLAGS -U__EMSCRIPTEN__"
+    unset EMSCRIPTEN
+  ])
 ])
 AS_IF([test "$host_os" = "nacl" -o "$host_os" = "pnacl"], [
   enable_asm="no"